[gmx-users] Re: Two questions when simulate the protein in lipid bilayer: 1. ratio of water/lipid; 2. ligand charge

[PeiQuan Chen]

Dear gmx-users-request:
  

Daan wrote:
>
>PRODRG now includes an algorithm which "distributes" formal charges over
>atoms in the molecule according to their relative electronegativities.
>On a test set of molecules, this approach gives an RMSD of (only) 0.1
>electron compared to charges calculated on the same test set of molecules
>with GAMESS.
>
>However - it is important to ensure protonation is correct, you can
>correct that with ADDHYD/DELHYD (see faq) commands *at the end* of your
>input file.
   I really want to know how to make a topol file of all-atom benzen. I think I can
use the ADDHYD commnads to implement it.

But when I input the follows, I got the error:

(ERRDRG> Atom C     referenced in instruction was not found.
PRODRG> Drug topology not made, sorry!)

HETATM    1  CAA DRG     1       0.590   2.790  -0.010  1.00 20.00             C
HETATM    2  CAB DRG     1       0.580   1.370   0.000  1.00 20.00             C
HETATM    3  CAD DRG     1       1.810   0.660   0.010  1.00 20.00             C
HETATM    4  CAF DRG     1       3.040   1.370   0.010  1.00 20.00             C
HETATM    5  CAE DRG     1       3.040   2.790   0.000  1.00 20.00             C
HETATM    6  CAC DRG     1       1.810   3.490  -0.010  1.00 20.00             C
END
ADDHYD C


Sincerely yours
---- 
PeiQuan Chen
________________________________________________________________________
PeiQuan Chen 	Department of Chemistry, Nankai University
WeiJin Road 94, TianJin, 300071, P.R.China
phone:	(86)2223506728		Mobile Phone: (+86)13920675030
gromacs at 163.com	
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++